Hey Mark,

You can still use the IM to upgrade even if you modified the default install directory to work in WAS. Here are some instructions I put together when upgrading from 1.0 to 1.0.1:

1.) Stop the RQM 1.0 jazz.war and help.war files and un-install them from WAS.
2.) Stop the WAS server.
3.) Delete the jazz_war and help_war folders under the /<WAS>/<ProfileName>/temp/<node>/<server>/ directory.
4.) Backup your RQM repository database according to your database vendor backup procedure.
5.) Using the IBM Installation Manager's "Update" feature, upgrade RQM from 1.0 to 1.0.1.
6.) Start the WAS server
7.) Install the RQM 1.0.1 jazz.war and help.war files in WAS and configure them using the exact same procedures as was done in the previous version.
8.) Navigate to https://<host>:9443/jazz/web/console/
9.) Import the Server Activation Key as well as the Client Access Licenses.
10.) Update the reports using the RQM Administration Client.
11.) Navigate to https://<host>:9443/jazz/web/console/QM and begin working in RQM 1.0.1.

To find more information on the manual procedure (e.g. using repotools to export/import your data instead of having the IM do it for you) check out the online help under "Installing and upgrading > Installing Rational Quality Manager > Installing Rational Quality Manager
Updating to v1.0.1 (manual database migration)"